Haplotype tree and heatmaps

root.dir <- here::here()
knitr::opts_chunk$set(echo = TRUE, root.dir=root.dir)
knitr::opts_knit$set(root.dir = root.dir)
knitr::opts_chunk$set(message = FALSE)
knitr::opts_chunk$set(warning = FALSE)

Introduction

The data/haplotype_amino.fas from haplotype analysis is used for generating phylogeneitic tree of the haplotypes and assessing correlation between haplotypes. Trees were calculated using hamming distance method which calculates pairwise distance matrix for corresponding residues between sequences of equal lengths. Corelation between haplotypes is assessed using heatmaply

Ploting of alignement haplotypes trees

library(adegenet)
library(ips)
library(ggplot2)
library(ggtree)
library(heatmaply)

nbin<-fasta2DNAbin("data/haplotypes_AA_names.fas")
an<-as.alignment(nbin)
nm<-as.matrix(an) 
nbinmat<-as.matrix(labels(nbin))
class(nbin)
dnbin<-dist.dna(nbin, model = "K80")
tree<-njs(dnbin)
ggt<-ggtree(tree, cex = 0.8, aes(color=branch.length))+scale_color_continuous(high='lightskyblue1',low='coral4')+geom_tiplab(align=TRUE, size=5)+geom_treescale(y = -1, color = "coral4", fontsize = 7)
njmsaplot<-msaplot(ggt, nbin, offset = 0.009, width=1, height = 0.5, color = c(rep("rosybrown", 1), rep("sienna1", 1), rep("lightgoldenrod1", 1), rep("lightskyblue1", 1)))

njmsaplot

pdf("figures/haplotype_tree.pdf", width = 11, height = 9, paper = "a4", pointsize=15)#save as pdf file
njmsaplot
dev.off()

Haplotype correlation heatmaps

sat2 <- NULL
for (i in 1:nrow(nm)) {
  sat2[i] <- paste(nm[i, ], collapse="")
}

sat2 <- toupper(sat2)
sat3 <- unique(sat2)
comat = matrix(nrow=length(sat3), ncol=length(sat3))
for (i in 1:length(sat3)) { 
  si <- sat3[i]
  for (j in 1:length(sat3)) { 
    sj <- sat3[j]
    difcnt = 0
    s1 = as.vector(strsplit(as.character(si), ""))
    s2 = as.vector(strsplit(as.character(sj), ""))
    for (k in 1:length(s1[[1]])) {
      if (s1[[1]][k] != s2[[1]][k]) {
        difcnt = difcnt + 1
      }
      comat[i, j] = difcnt
      #print(paste(i, " ", j, " ", difcnt))
    }
  }
}
#comat  is Hamming distance matrix
colnames(comat)<-nbinmat

heatmap<-heatmaply_cor(cor(comat), file= "figures/heatmap.pdf",  xlab= "haplotypes", ylab="haplotypes",
              k_col=3,
              k_row=3, margins =c(10,10,15), fontsize_row = 8,
              fontsize_col = 8)

heatmap

Figures are available haplotypes_trees and Haplotype_correlations

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